GABPA.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GABPA.H12RSNP.0.PSM.A
Gene (human)	GABPA (GeneCards)
Gene synonyms (human)	E4TF1A
Gene (mouse)	Gabpa
Gene synonyms (mouse)	E4tf1a
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	13
Consensus	nvSCGGAAGYdvv
GC content	62.03%
Information content (bits; total / per base)	14.186 / 1.091
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	997

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Human	36 (228)	0.968	0.982	0.936	0.968	0.946	0.969	4.333	4.918	347.27	447.143
Mouse	5 (33)	0.975	0.991	0.948	0.98	0.961	0.974	4.479	4.793	268.092	453.42

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.999	0.997	0.998	0.996	0.995	0.993
Overall, 2 experiments	best	0.999	0.998	0.999	0.997	0.997	0.996
Methyl HT-SELEX, 1 experiments	median	0.999	0.998	0.999	0.997	0.997	0.996
Methyl HT-SELEX, 1 experiments	best	0.999	0.998	0.999	0.997	0.997	0.996
Non-Methyl HT-SELEX, 1 experiments	median	0.998	0.997	0.997	0.995	0.993	0.99
Non-Methyl HT-SELEX, 1 experiments	best	0.998	0.997	0.997	0.995	0.993	0.99

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	7.238	12.751	0.238	0.182

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Tryptophan cluster factors {3.5} (TFClass)
TF family	Ets-related {3.5.2} (TFClass)
TF subfamily	ETS-like {3.5.2.1} (TFClass)
TFClass ID	TFClass: 3.5.2.1.5
HGNC	HGNC:4071
MGI	MGI:95610
EntrezGene (human)	GeneID:2551 (SSTAR profile)
EntrezGene (mouse)	GeneID:14390 (SSTAR profile)
UniProt ID (human)	GABPA_HUMAN
UniProt ID (mouse)	GABPA_MOUSE
UniProt AC (human)	Q06546 (TFClass)
UniProt AC (mouse)	Q00422 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	36 human, 5 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	GABPA.H12RSNP.0.PSM.A.pcm
PWM	GABPA.H12RSNP.0.PSM.A.pwm
PFM	GABPA.H12RSNP.0.PSM.A.pfm
Alignment	GABPA.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	GABPA.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	GABPA.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	GABPA.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	GABPA.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	GABPA.H12RSNP.0.PSM.A_homer_format_0.001.txt GABPA.H12RSNP.0.PSM.A_homer_format_0.0005.txt GABPA.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	320.0	263.0	283.0	131.0
02	441.0	165.0	357.0	34.0
03	75.0	752.0	163.0	7.0
04	58.0	938.0	1.0	0.0
05	1.0	1.0	995.0	0.0
06	0.0	0.0	997.0	0.0
07	992.0	1.0	2.0	2.0
08	995.0	1.0	0.0	1.0
09	51.0	8.0	937.0	1.0
10	47.0	155.0	26.0	769.0
11	169.0	112.0	588.0	128.0
12	264.0	277.0	392.0	64.0
13	210.0	419.0	207.0	161.0

PFM

	A	C	G	T
01	0.321	0.264	0.284	0.131
02	0.442	0.165	0.358	0.034
03	0.075	0.754	0.163	0.007
04	0.058	0.941	0.001	0.0
05	0.001	0.001	0.998	0.0
06	0.0	0.0	1.0	0.0
07	0.995	0.001	0.002	0.002
08	0.998	0.001	0.0	0.001
09	0.051	0.008	0.94	0.001
10	0.047	0.155	0.026	0.771
11	0.17	0.112	0.59	0.128
12	0.265	0.278	0.393	0.064
13	0.211	0.42	0.208	0.161

PWM

	A	C	G	T
01	0.248	0.053	0.126	-0.637
02	0.568	-0.409	0.357	-1.949
03	-1.185	1.1	-0.421	-3.359
04	-1.436	1.32	-4.522	-4.979
05	-4.522	-4.522	1.379	-4.979
06	-4.979	-4.979	1.381	-4.979
07	1.376	-4.522	-4.21	-4.21
08	1.379	-4.522	-4.979	-4.522
09	-1.56	-3.251	1.319	-4.522
10	-1.639	-0.471	-2.203	1.122
11	-0.385	-0.792	0.854	-0.66
12	0.057	0.105	0.45	-1.34
13	-0.17	0.517	-0.184	-0.433

Standard thresholds

P-value	Threshold
0.001	2.62721
0.0005	3.96966
0.0001	6.82972